| event | clusterid | feature | mfi | |
|---|---|---|---|---|
| Min. : 776 | Length:242919 | Length:242919 | Min. :-2.6612 | |
| 1st Qu.: 7914 | Class :character | Class :character | 1st Qu.: 0.4337 | |
| Median :14196 | Mode :character | Mode :character | Median : 2.4066 | |
| Mean :16810 | NA | NA | Mean : 2.3807 | |
| 3rd Qu.:24155 | NA | NA | 3rd Qu.: 4.2198 | |
| Max. :47309 | NA | NA | Max. : 6.3943 |
Background
In this analysis workflow we use spectral flow cytometry to simultaneously assess histone H3 post-translational modifications (H3-PTMs) at the single-cell level, in the context of cell cycle status and cell-type-specific markers. This workflow was implemented in BioProtocol Exchange by Golden et al., 2024 and contains supplementary figures and data analysis associated with the pre-print.
Information about biological material
iPSC-derived Neuronal Progenitor Cells (NPCs) were generated using the female control line SCTi003-A (Stem Cell Technologies). NPC induction was performed with the STEMdiff SMADi Neural Induction Kit, following the manufacturer’s instructions. All experiments were conducted with three biological replicates, defined in this context as NPCs induced in three independent wells. For further details on experimental design and data acquisition, please refer to Golden et al., 2024.
Information about initial data processing performed in OMIQ
| Data processing | Strategy | Additional Information |
|---|---|---|
| Scaling | Hyperbolic arcsine (arcsinh) | Finak et al., 2010 |
| Gating | Cell QC and manual gating for comparison | Golden et al., 2024 |
| Subsetting | Fully stained samples | Removal of single color controls and blanks to prevent noise in downstream analysis |
| Subsampling | Random downsampling. Equal number of cells available in the Live Cells filter | Braanker et al., 2021 Note: Density-dependent downsampling strategy should be tested to assess if there is loss of small cell populations due to random cell selection Qiu, 2017 |
| Dimension Reduction | PCA | all features |
| Dimension Reduction | opt-SNE | selected features |
| Clustering | FlowSOM | selected features |
Data analysis and visualization
The goal of this analysis is to assess H3-PTM signatures in NPCs in the context of their cell cycle status and lineage markers (PAX6 in this case).
Note
I named the fluorescence intensity column as mfi and it is misleading. Note that this is not the median value but the fluorescence value of each feature in each cell.
| event | clusterid | feature | mfi | mfi_z.V1 | |
|---|---|---|---|---|---|
| Min. : 776 | Length:242919 | Length:242919 | Min. :-2.6612 | Min. :-2.6246340 | |
| 1st Qu.: 7914 | Class :character | Class :character | 1st Qu.: 0.4337 | 1st Qu.:-1.0135128 | |
| Median :14196 | Mode :character | Mode :character | Median : 2.4066 | Median : 0.0135043 | |
| Mean :16810 | NA | NA | Mean : 2.3807 | Mean : 0.0000000 | |
| 3rd Qu.:24155 | NA | NA | 3rd Qu.: 4.2198 | 3rd Qu.: 0.9573996 | |
| Max. :47309 | NA | NA | Max. : 6.3943 | Max. : 2.0893763 |
Z-score column was added to data
Goal: Assess H3-PTM values in the context of cell cycle status and markers such us cleaved-Caspase3 and PAX6. This section also aims to compare FlowSOM unsupervised clustering and manual gates.
Note
In the context of this project (and most spectral data) the targets of the antibodies are referred to as features. Gates, whether manual or created through FlowSOM, are referred to as filters.
Initial visualization of all events within each cluster
This plot allows visualization of single events in each cluster. Not included in Methods paper
Adapted from Heatmap for time series
Show code
p <-ggplot(df,aes(event,feature,fill=mfi_z))+
geom_tile(color= "white",linewidth=0.000000001) +
scale_fill_viridis(name="Scaled Fluorescense",
alpha = 1,
begin = 0,
end = 1,
direction = 1,
discrete = FALSE,
option = "C",
aesthetics = "fill")
p <-p + facet_grid(~clusterid, scales = "free", space = "free",)
p <-p + scale_y_discrete(limits = rev(levels(df$feature))) # Reverse the order of the factor levels for y-axis
p <-p + scale_x_discrete(labels = NULL)
p <-p + theme_minimal(base_size = 8)
p <-p + labs(title= paste("Fluorescence intentisity values of each feature by fsom cluster | NPC"), x="Event", y="Feature")
p <-p + theme(legend.position = "bottom")+
theme(plot.title=element_text(size = 14))+
theme(axis.text.y=element_text(size=6)) +
theme(strip.background = element_rect(colour="white"))+
theme(plot.title=element_text(hjust=0))+
theme(axis.ticks=element_blank())+
theme(axis.text=element_text(size=7))+
theme(legend.title=element_text(size=8))+
theme(legend.text=element_text(size=6))+
theme(strip.text.x = element_text(angle = 90, hjust = 1)) + # Rotate the cluster id labels
removeGrid()#ggExtra
# you will want to expand your plot screen before this bit!
p
Heatmap visualization of concatenated files
For this plot, we used heatmap data downloaded from OMIQ, which includes three concatenated biological replicates. To compare the resolution between FSOM clusters and manual gating, data will be plotted for both sets of filters.
| H3K14ac | phH3_S10 | H3K4me3 | Total.H3 | Caspase3 | PAX6 | H3K27ac | H3K9ac | FxCycle | |
|---|---|---|---|---|---|---|---|---|---|
| fsom05 | 0.38 | 0.03 | 5.13 | 1.52 | -0.55 | 2.62 | 3.97 | 4.81 | 4.52 |
| fsom08 | 0.46 | 0.22 | 4.83 | 1.56 | -0.04 | 2.56 | 3.44 | 4.41 | 3.61 |
| fsom06 | 0.63 | 0.39 | 5.17 | 1.94 | -0.17 | 3.15 | 4.12 | 5.02 | 4.04 |
| fsom13 | 0.47 | 0.18 | 4.96 | 1.71 | 1.44 | 2.59 | 3.70 | 4.55 | 4.07 |
| fsom12 | 0.48 | 0.24 | 4.85 | 1.49 | 2.72 | 1.65 | 3.11 | 4.28 | 3.76 |
| fsom11 | 0.13 | 0.18 | 3.89 | 0.57 | 4.76 | 0.76 | 2.07 | 2.07 | 3.64 |
| H3K14ac | phH3_S10 | H3K4me3 | Total.H3 | Caspase3 | PAX6 | H3K27ac | H3K9ac | FxCycle | |
|---|---|---|---|---|---|---|---|---|---|
| fsom01 | 1.66 | 5.41 | 5.55 | 1.99 | -0.58 | -1.57 | 4.05 | 4.71 | 4.62 |
| Apoptotic Cells | 0.15 | 0.18 | 4.03 | 0.61 | 4.69 | 0.85 | 2.18 | 2.23 | 3.66 |
| Other/G0/G1 | 0.42 | 0.19 | 4.91 | 1.51 | -0.09 | 1.19 | 3.27 | 4.26 | 3.74 |
| fsom13 | 0.47 | 0.18 | 4.96 | 1.71 | 1.44 | 2.59 | 3.70 | 4.55 | 4.07 |
| fsom06 | 0.63 | 0.39 | 5.17 | 1.94 | -0.17 | 3.15 | 4.12 | 5.02 | 4.04 |
| fsom03 | 0.36 | 0.07 | 5.09 | 1.50 | -0.44 | 1.10 | 3.59 | 4.48 | 4.37 |
Features MFI by fsom clusters
Hierarchical Clustering (hclust)
Initial assessment through hierarchical clustering
Show code
[1] "#324DA0FF" "#008EA8FF" "#69BBABFF" "#C9DDC9FF" "#FEFDBEFF" "#F4D481FF"
[7] "#EB9D00FF" "#DE5400FF" "#A51122FF"Show code
# Sort dendogram nodes
row_dend = dendsort(hclust(dist(df_m)))
col_dend = dendsort(hclust(dist(t(df_m))))
# Plot heatmap
h1 <- Heatmap(df_m, name = "MFI",
row_title_rot = 0,
row_names_gp = gpar(fontsize = 8), # Set row name font size
column_names_gp = gpar(fontsize = 8), # Set column name font size
col = col_1,
rect_gp = gpar(col = "white", lwd = 0.5),
cluster_rows = row_dend,
cluster_columns = col_dend,
row_split = 2, column_split = 2,
row_gap = unit(0.5, "mm"), column_gap = unit(0.5, "mm"), border = TRUE,
column_title = "MFI Values Across NPC Clusters Identified by FlowSOM | hclust",
column_title_gp = gpar(fontsize = 8, fontface = "bold"),
cell_fun = function(j, i, x, y, width, height, fill) {
grid.text(sprintf("%.1f", df_m[i, j]), x, y, gp = gpar(fontsize = 5)) # Add text inside cells
})
h1
quartz_off_screen
2 quartz_off_screen
2 Pearson Correlation
Useful to cluster data based on the correlation between features rather than their absolute differences. It’s particularly good for identifying clusters with similar expression patterns across different markers, regardless of absolute values.
Show code
[1] "#324DA0FF" "#008EA8FF" "#69BBABFF" "#C9DDC9FF" "#FEFDBEFF" "#F4D481FF"
[7] "#EB9D00FF" "#DE5400FF" "#A51122FF"Show code
# Plot heatmap
# Create the heatmap with Pearson correlation as the distance metric
set.seed(135)
h2 <- Heatmap(df_m, name = "MFI",
clustering_distance_rows = "pearson", # Use Pearson correlation for row clustering
clustering_method_rows = "complete", # Specify the clustering method (e.g., complete linkage)
row_km = 4, row_km_repeats = 100,
row_title_rot = 0,
row_names_gp = gpar(fontsize = 9), # Set row name font size
column_names_gp = gpar(fontsize = 9), # Set column name font size
col = col_1,
row_gap = unit(1, "mm"), border = TRUE,
column_title = "MFI Values Across NPC Clusters Identified by FlowSOM | pearson",
column_title_gp = gpar(fontsize = 8, fontface = "bold"),
cell_fun = function(j, i, x, y, width, height, fill) {
grid.text(sprintf("%.1f", df_m[i, j]), x, y, gp = gpar(fontsize = 7)) # Add text inside cells
})
h2
quartz_off_screen
2 quartz_off_screen
2 Features MFI in manual gates
Show code
[1] "#3C5941FF" "#3C5941FF" "#758A68FF" "#B4BD93FF" "#FBF2C4FF" "#E3C28DFF"
[7] "#D48E53FF" "#C7522BFF" "#C7522BFF"Show code
# Sort dendogram nodes
row_dend = dendsort(hclust(dist(dfg_m)))
col_dend = dendsort(hclust(dist(t(dfg_m))))
# Plot heatmap
h1g <- Heatmap(dfg_m, name = "MFI",
col = col_fall,
rect_gp = gpar(col = "white", lwd = 0.5),
cluster_rows = row_dend,
cluster_columns = col_dend,
row_split = 7, column_split = 2,
row_gap = unit(1, "mm"), column_gap = unit(1, "mm"), border = TRUE,
column_title = "NPC MFI by manual gating | hclust")
h1g
quartz_off_screen
2 quartz_off_screen
2 This data viz strategy aims to highlight the contributions of each feature to different filters (aka clusters).
Prepare data
Show code
# Prepare data
cbp <- data_long
# Convert relevant columns to factors
cbp <- cbp %>%
mutate(
feature = factor(feature),
clusterid = factor(clusterid),
event = factor(event),
mfi_shifted = mfi + abs(min(mfi)) + 1 # Shift MFI (not scaled) values to avoid negatives
)
summary_cbp <- summary(cbp)
kable(summary_cbp, format = "html", caption = "Summary of data containing shifted values")| event | clusterid | feature | mfi | mfi_shifted | |
|---|---|---|---|---|---|
| 2595 : 27 | fsom08 :58752 | Caspase3:26991 | Min. :-2.6612 | Min. : 1.000 | |
| 2605 : 27 | fsom07 :43623 | FxCycle :26991 | 1st Qu.: 0.4337 | 1st Qu.: 4.095 | |
| 2613 : 27 | fsom05 :32031 | H3K14ac :26991 | Median : 2.4066 | Median : 6.068 | |
| 2623 : 27 | fsom06 :31950 | H3K27ac :26991 | Mean : 2.3807 | Mean : 6.042 | |
| 2681 : 27 | fsom02 :25830 | H3K4me3 :26991 | 3rd Qu.: 4.2198 | 3rd Qu.: 7.881 | |
| 2685 : 27 | fsom03 :23085 | H3K9ac :26991 | Max. : 6.3943 | Max. :10.056 | |
| (Other):242757 | (Other):27648 | (Other) :80973 | NA | NA |
Features contributions to each cluster
To assess circular barplots for all clusters, please go to the output folder.
Show code
cbp2 <- cbp1 +
# Add labels
labs(
title = "\nContribution of individual features to cluster fsom 14",
subtitle = paste(
"\nMFI values were shifted to ensure positivity, then summarized",
"by feature within each cluster, displaying maximum, minimum, and median MFI values.\n",
sep = "\n"
)) +
# Customize general theme
theme(
# Set default color and font family for the text
text = element_text(color = "gray12"),
# Customize the text in the title, subtitle, and caption
plot.title = element_text(face = "bold", size = 12, hjust = 0),
plot.subtitle = element_text(size = 8, hjust = 0),
# Make the background white and remove extra grid lines
panel.background = element_rect(fill = "white", color = "white"),
panel.grid = element_blank(),
panel.grid.major.x = element_blank()
)
# Use `ggsave("plot.png", plt, width=9, height=12.6)` to save it as in the output
cbp2
Show code
ggsave("output/PNG/bar_plot_fsom14.png", cbp2,width=9, height=12.6)
ggsave(filename = "output/SVG/bar_plot_fsom14.svg", plot = cbp2, width = 9, height = 12.6)Goal: Assessment of possible correlations between cell cycle progression, DNA content, H3 content and lineage markers
Correlation between phS10-H3 and DNA content
Goal: Assess phS10H3 and DNA content dynamics
Show code
crp <- data # bring back data without re-shaping to long format
# filter features of interest
filtered_data <- crp %>%
select(FxCycle, phH3_S10, `Total H3`, clusterid, PAX6) %>%
rename(H3 = `Total H3`)
# Step 1: Calculate mean PAX6 intensity and correlation for each cluster
cluster_stats <- filtered_data %>%
group_by(clusterid) %>%
summarize(mean_PAX6 = mean(PAX6, na.rm = TRUE),
correlation = cor(FxCycle, phH3_S10, method = "pearson")) %>%
arrange(desc(mean_PAX6), correlation) # Sort by mean PAX6 (descending) and then by correlation
# Step 2: Reorder the clusterid factor based on combined ordering
filtered_data <- filtered_data %>%
mutate(clusterid = factor(clusterid, levels = cluster_stats$clusterid))
# Step 3: Merge the correlation data with the filtered data
filtered_data <- filtered_data %>%
left_join(cluster_stats, by = "clusterid")
# Step 4: Create the plot with the Pearson correlation as a label inside each facet
bub1 <- filtered_data %>%
arrange(desc(H3)) %>%
ggplot(aes(x = FxCycle, y = phH3_S10, size = H3, fill = PAX6)) +
geom_point(alpha = 0.4, shape = 21, color = "black") + # Black contour with shape 21
scale_size(range = c(-1, 5), name = "H3 Fluorescence") +
scale_fill_viridis_c(option = "D", name = "PAX6 Intensity") + # Fill by PAX6 intensity
theme_ipsum() +
labs(
title="Correlation between DNA content and Phospho S10 H3",
subtitle="Clusters are ordered by PAX6 intensity and Pearson correlation value",
) +
theme(legend.position = "bottom",
panel.background = element_rect(fill = "white", color = "white"),
panel.border = element_rect(fill = NA, color = "darkgray"),
plot.background = element_rect(fill = "white", color = "white"),
panel.grid = element_blank(),
panel.grid.major = element_blank()
) +
ylab("Phospho H3 S10 Fluorescence") +
xlab("FxCycle (DNA Content)") +
facet_wrap(~ clusterid) + # Use scales="free" to adjust each facet independently
geom_text(aes(label = sprintf("r = %.2f", correlation)),
x = -Inf, y = Inf, hjust = -0.1, vjust = 1.1, size = 3, color = "black")
bub1
Show code
ggsave("output/PNG/correlation_plot1.png", bub1,width=14, height=12)
ggsave(filename = "output/SVG/correlation_plot1.svg", plot = bub1, width = 14, height = 12)Correlation between lineage marker and Caspase-3
Background: Caspase activity mediates the differentiation of embryonic stem cells
Show code
crp2 <- data # bring back data without re-shaping to long format
# filter features of interest
filtered_data2 <- crp2 %>%
select(FxCycle, phH3_S10, Caspase3, clusterid, PAX6)
# Step 1: Calculate mean PAX6 intensity and correlation for each cluster
cluster_stats2 <- filtered_data2 %>%
group_by(clusterid) %>%
summarize(mean_FxCycle = mean(FxCycle, na.rm = TRUE),
correlation = cor(Caspase3, PAX6, method = "pearson")) %>%
arrange(desc(mean_FxCycle), correlation) # Sort by mean PAX6 (descending) and then by correlation
# Step 2: Reorder the clusterid factor based on combined ordering
filtered_data2 <- filtered_data2 %>%
mutate(clusterid = factor(clusterid, levels = cluster_stats2$clusterid))
# Step 3: Merge the correlation data with the filtered data
filtered_data2 <- filtered_data2 %>%
left_join(cluster_stats2, by = "clusterid")
# Step 4: Create the plot with the Pearson correlation as a label inside each facet
bub2 <- filtered_data2 %>%
arrange(desc(phH3_S10)) %>%
ggplot(aes(x = PAX6, y = Caspase3, size = FxCycle, fill = phH3_S10)) +
geom_point(alpha = 0.4, shape = 21, color = "black") + # Black contour with shape 21
scale_size(range = c(-1, 5), name = "Cell Cycle") +
scale_fill_viridis_c(option = "D", name = "Mitosis | phH3_S10") +
theme_ipsum() +
labs(
title="Correlation between lineage commitment marker and cleaved-Caspase3",
subtitle="Clusters are ordered by FxCycle intensity and Person correlation value",
) +
theme(legend.position = "bottom",
panel.background = element_rect(fill = "white", color = "white"),
panel.border = element_rect(fill = NA, color = "darkgray"),
plot.background = element_rect(fill = "white", color = "white"),
panel.grid = element_blank(),
panel.grid.major = element_blank()
) +
ylab("Cleaved-Caspase3 Fluorescence") +
xlab("PAX6 Fluorescense") +
facet_wrap(~ clusterid) + # Use scales="free" to adjust each facet independently
geom_text(aes(label = sprintf("r = %.2f", correlation)),
x = -Inf, y = Inf, hjust = -0.1, vjust = 1.1, size = 3, color = "black")
bub2
Show code
ggsave("output/PNG/correlation_plot2.png", bub2,width=14, height=12)
ggsave(filename = "output/SVG/correlation_plot2.svg", plot = bub2, width = 14, height = 12)Goal: Assessment of the distributions of each H3-PTM within clusters.
From R Gallery
Density plots
Density plots for fsom clusters
Show code
# Represent all density plots in the same axis
d1 <- df %>%
filter(feature %in% c("H3K9ac", "H3K14ac", "H3K27ac", "H3K4me3")) %>%
ggplot( aes(x=mfi_z, fill=feature)) +
geom_density( color="#e9ecef", alpha=0.6) +
scale_fill_manual(values=pal2) +
facet_wrap(~clusterid, ncol = 3, scales = "free_y") +
labs(title = "Density Plots: Feature distribution per cluster", x = "Scaled Fluorescence", y = "Density") +
theme_minimal() +
theme(legend.position = "bottom",
plot.title = element_text(size = 12, hjust = 0),
axis.text.y = element_text(size = 8),
axis.ticks = element_blank(),
axis.text = element_text(size = 8),
legend.title = element_text(size = 10),
legend.text = element_text(size = 8),
legend.key.size = unit(0.5, "lines"), # Reduce size of boxes in legend
panel.spacing = unit(0.05, "lines"),
panel.grid = element_blank(),
strip.text = element_text(size = 8)) +
labs(fill = "Features")
ggsave("output/PNG/density_plot_1.png", width = 30, height = 15, units = "cm", dpi = 600)
ggsave("output/SVG/density_plot_1.svg", plot = d1, width = 7, height = 7)Density plots for manual gates
# A tibble: 6 × 4
event clusterid feature mfi
<dbl> <chr> <chr> <dbl>
1 2595 fsom06 FxCycle 4.46
2 2596 fsom04 FxCycle 4.40
3 2598 fsom06 FxCycle 3.97
4 2600 fsom05 FxCycle 4.53
5 2601 fsom05 FxCycle 4.30
6 2602 fsom03 FxCycle 4.28Show code
# Represent all density plots in the same axis
d1g <- dfg %>%
filter(feature %in% c("H3K9ac", "H3K14ac", "H3K27ac", "H3K4me3")) %>%
ggplot( aes(x=mfi_z, fill=feature)) +
geom_density( color="#e9ecef", alpha=0.6) +
scale_fill_manual(values=pal2) +
facet_wrap(~clusterid, ncol = 3, scales = "free_y") +
labs(title = "Density Plots: Feature distribution per cluster", x = "Scaled Fluorescence", y = "Density") +
theme_minimal() +
theme(legend.position = "bottom",
plot.title = element_text(size = 12, hjust = 0),
axis.text.y = element_text(size = 8),
axis.ticks = element_blank(),
axis.text = element_text(size = 8),
legend.title = element_text(size = 10),
legend.text = element_text(size = 8),
legend.key.size = unit(0.5, "lines"), # Reduce size of boxes in legend
panel.spacing = unit(0.05, "lines"),
panel.grid = element_blank(),
strip.text = element_text(size = 8)) +
labs(fill = "Features")
ggsave("output/PNG/density_gate_plot_1.png", width = 30, height = 15, units = "cm", dpi = 600)
ggsave("output/SVG/density_gate_plot_1.svg", plot = d1, width = 7, height = 7)Histograms
From R Gallery
Histograms allow direct visualization of cell count.
Histograms for fsom clusters
Show code
histogram1 <- df %>%
filter(feature %in% c("H3K9ac", "H3K14ac", "H3K27ac", "H3K4me3")) %>%
ggplot(aes(x = mfi, fill = feature)) +
geom_histogram(binwidth = 0.2, color = "#e9ecef", alpha = 0.6, position = 'identity') +
scale_fill_manual(values = c("#8650a6", "#ac9c3d", "#6881d8", "#ba543d")) +
facet_wrap(~clusterid, ncol = 3, scales = "free_y") +
labs(title = "Histograms: Feature distribution per cluster", x = "Fluorescence", y = "Cell count") +
theme_minimal() +
theme(legend.position = "bottom",
plot.title = element_text(size = 12, hjust = 0),
axis.text.y = element_text(size = 6),
axis.ticks = element_blank(),
axis.text = element_text(size = 7),
legend.title = element_text(size = 10),
legend.text = element_text(size = 8),
legend.key.size = unit(0.5, "lines"), # Reduce size of boxes in legend
panel.spacing = unit(0.05, "lines"),
panel.grid = element_blank(),
strip.text = element_text(size = 8)) +
labs(fill = "Features")
ggsave("output/PNG/histogram_plot_1.png", width = 30, height = 15, units = "cm", dpi = 600)
ggsave("output/SVG/histogram_plot_1.svg", plot = histogram1, width = 7, height = 7)Histograms for manual gates and fsom clusters
Show code
histogram_gates <- dfg %>%
filter(feature %in% c("H3K9ac", "H3K14ac", "H3K27ac", "H3K4me3")) %>%
ggplot(aes(x = mfi, fill = feature)) +
geom_histogram(binwidth = 0.2, color = "#e9ecef", alpha = 0.6, position = 'identity') +
scale_fill_manual(values = c("#8650a6", "#ac9c3d", "#6881d8", "#ba543d")) +
facet_wrap(~clusterid, ncol = 3, scales = "free_y") +
labs(title = "Histograms: Feature distribution per manual cluster", x = "Fluorescence", y = "Cell count") +
theme_minimal() +
theme(legend.position = "bottom",
plot.title = element_text(size = 12, hjust = 0),
axis.text.y = element_text(size = 6),
axis.ticks = element_blank(),
axis.text = element_text(size = 7),
legend.title = element_text(size = 10),
legend.text = element_text(size = 8),
legend.key.size = unit(0.5, "lines"), # Reduce size of boxes in legend
panel.spacing = unit(0.05, "lines"),
panel.grid = element_blank(),
strip.text = element_text(size = 8)) +
labs(fill = "Features")
ggsave("output/PNG/histogram_gates_plot_1.png", width = 30, height = 15, units = "cm", dpi = 600)
ggsave("output/SVG/histogram_gates_plot_1.svg", plot = histogram_gates, width = 7, height = 7)Violin plots
Goal: To assess the distribution of features, median fluorescence intensity values, and effect sizes within each fsom cluster
To make this plots I used ggstatsplot. I have to admit this package has my favorite vignette of all times.
Pairwise comparisons
Extracting pairwise comparisons (post-hoc test = Dunn)
| group1 | group2 | statistic | p.value | alternative | distribution | p.adjust.method | test | expression | ClusterID | Significance |
|---|---|---|---|---|---|---|---|---|---|---|
| FxCycle | H3K14ac | 8.5461719 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom01 | Less than 0.05 |
| FxCycle | H3K27ac | 3.4392033 | 0.0006732 | two.sided | z | FDR | Dunn | list, it.... | fsom01 | Less than 0.05 |
| FxCycle | H3K4me3 | 8.2743578 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom01 | Less than 0.05 |
| FxCycle | H3K9ac | 0.3304748 | 0.7410412 | two.sided | z | FDR | Dunn | list, it.... | fsom01 | More than 0.05 |
| FxCycle | phH3_S10 | 6.4750415 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom01 | Less than 0.05 |
| H3K14ac | H3K27ac | 5.1069686 | 0.0000004 | two.sided | z | FDR | Dunn | list, it.... | fsom01 | Less than 0.05 |
| H3K14ac | H3K4me3 | 16.8205298 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom01 | Less than 0.05 |
| H3K14ac | H3K9ac | 8.8766468 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom01 | Less than 0.05 |
| H3K14ac | phH3_S10 | 15.0212134 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom01 | Less than 0.05 |
| H3K27ac | H3K4me3 | 11.7135611 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom01 | Less than 0.05 |
| H3K27ac | H3K9ac | 3.7696781 | 0.0002043 | two.sided | z | FDR | Dunn | list, it.... | fsom01 | Less than 0.05 |
| H3K27ac | phH3_S10 | 9.9142448 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom01 | Less than 0.05 |
| H3K4me3 | H3K9ac | 7.9438830 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom01 | Less than 0.05 |
| H3K4me3 | phH3_S10 | 1.7993164 | 0.0771093 | two.sided | z | FDR | Dunn | list, it.... | fsom01 | More than 0.05 |
| H3K9ac | phH3_S10 | 6.1445666 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom01 | Less than 0.05 |
| FxCycle | H3K14ac | 42.6818424 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom02 | Less than 0.05 |
| FxCycle | H3K27ac | 10.4908009 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom02 | Less than 0.05 |
| FxCycle | H3K4me3 | 44.9863645 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom02 | Less than 0.05 |
| FxCycle | H3K9ac | 24.5207285 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom02 | Less than 0.05 |
| FxCycle | phH3_S10 | 59.0166863 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom02 | Less than 0.05 |
| H3K14ac | H3K27ac | 32.1910415 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom02 | Less than 0.05 |
| H3K14ac | H3K4me3 | 87.6682069 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom02 | Less than 0.05 |
| H3K14ac | H3K9ac | 67.2025709 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom02 | Less than 0.05 |
| H3K14ac | phH3_S10 | 16.3348439 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom02 | Less than 0.05 |
| H3K27ac | H3K4me3 | 55.4771654 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom02 | Less than 0.05 |
| H3K27ac | H3K9ac | 35.0115294 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom02 | Less than 0.05 |
| H3K27ac | phH3_S10 | 48.5258854 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom02 | Less than 0.05 |
| H3K4me3 | H3K9ac | 20.4656360 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom02 | Less than 0.05 |
| H3K4me3 | phH3_S10 | 104.0030508 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom02 | Less than 0.05 |
| H3K9ac | phH3_S10 | 83.5374148 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom02 | Less than 0.05 |
| FxCycle | H3K14ac | 51.4064460 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom03 | Less than 0.05 |
| FxCycle | H3K27ac | 23.1193160 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom03 | Less than 0.05 |
| FxCycle | H3K4me3 | 28.1355094 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom03 | Less than 0.05 |
| FxCycle | H3K9ac | 5.4927044 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom03 | Less than 0.05 |
| FxCycle | phH3_S10 | 67.3914008 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom03 | Less than 0.05 |
| H3K14ac | H3K27ac | 28.2871301 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom03 | Less than 0.05 |
| H3K14ac | H3K4me3 | 79.5419554 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom03 | Less than 0.05 |
| H3K14ac | H3K9ac | 56.8991505 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom03 | Less than 0.05 |
| H3K14ac | phH3_S10 | 15.9849547 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom03 | Less than 0.05 |
| H3K27ac | H3K4me3 | 51.2548253 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom03 | Less than 0.05 |
| H3K27ac | H3K9ac | 28.6120204 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom03 | Less than 0.05 |
| H3K27ac | phH3_S10 | 44.2720848 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom03 | Less than 0.05 |
| H3K4me3 | H3K9ac | 22.6428050 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom03 | Less than 0.05 |
| H3K4me3 | phH3_S10 | 95.5269101 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom03 | Less than 0.05 |
| H3K9ac | phH3_S10 | 72.8841052 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom03 | Less than 0.05 |
| FxCycle | H3K14ac | 37.9459530 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom04 | Less than 0.05 |
| FxCycle | H3K27ac | 14.9266393 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom04 | Less than 0.05 |
| FxCycle | H3K4me3 | 23.1354709 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom04 | Less than 0.05 |
| FxCycle | H3K9ac | 6.1605892 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom04 | Less than 0.05 |
| FxCycle | phH3_S10 | 47.6216510 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom04 | Less than 0.05 |
| H3K14ac | H3K27ac | 23.0193137 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom04 | Less than 0.05 |
| H3K14ac | H3K4me3 | 61.0814239 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom04 | Less than 0.05 |
| H3K14ac | H3K9ac | 44.1065422 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom04 | Less than 0.05 |
| H3K14ac | phH3_S10 | 9.6756980 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom04 | Less than 0.05 |
| H3K27ac | H3K4me3 | 38.0621102 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom04 | Less than 0.05 |
| H3K27ac | H3K9ac | 21.0872285 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom04 | Less than 0.05 |
| H3K27ac | phH3_S10 | 32.6950117 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom04 | Less than 0.05 |
| H3K4me3 | H3K9ac | 16.9748817 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom04 | Less than 0.05 |
| H3K4me3 | phH3_S10 | 70.7571219 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom04 | Less than 0.05 |
| H3K9ac | phH3_S10 | 53.7822402 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom04 | Less than 0.05 |
| FxCycle | H3K14ac | 58.8688359 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom05 | Less than 0.05 |
| FxCycle | H3K27ac | 22.5157168 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom05 | Less than 0.05 |
| FxCycle | H3K4me3 | 29.8483946 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom05 | Less than 0.05 |
| FxCycle | H3K9ac | 12.2922393 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom05 | Less than 0.05 |
| FxCycle | phH3_S10 | 77.4453634 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom05 | Less than 0.05 |
| H3K14ac | H3K27ac | 36.3531191 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom05 | Less than 0.05 |
| H3K14ac | H3K4me3 | 88.7172305 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom05 | Less than 0.05 |
| H3K14ac | H3K9ac | 71.1610752 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom05 | Less than 0.05 |
| H3K14ac | phH3_S10 | 18.5765275 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom05 | Less than 0.05 |
| H3K27ac | H3K4me3 | 52.3641114 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom05 | Less than 0.05 |
| H3K27ac | H3K9ac | 34.8079561 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom05 | Less than 0.05 |
| H3K27ac | phH3_S10 | 54.9296466 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom05 | Less than 0.05 |
| H3K4me3 | H3K9ac | 17.5561553 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom05 | Less than 0.05 |
| H3K4me3 | phH3_S10 | 107.2937580 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom05 | Less than 0.05 |
| H3K9ac | phH3_S10 | 89.7376027 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom05 | Less than 0.05 |
| FxCycle | H3K14ac | 43.5682774 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom06 | Less than 0.05 |
| FxCycle | H3K27ac | 5.2058828 | 0.0000002 | two.sided | z | FDR | Dunn | list, it.... | fsom06 | Less than 0.05 |
| FxCycle | H3K4me3 | 49.8409508 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom06 | Less than 0.05 |
| FxCycle | H3K9ac | 40.6870455 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom06 | Less than 0.05 |
| FxCycle | phH3_S10 | 54.5065527 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom06 | Less than 0.05 |
| H3K14ac | H3K27ac | 48.7741602 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom06 | Less than 0.05 |
| H3K14ac | H3K4me3 | 93.4092282 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom06 | Less than 0.05 |
| H3K14ac | H3K9ac | 84.2553229 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom06 | Less than 0.05 |
| H3K14ac | phH3_S10 | 10.9382753 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom06 | Less than 0.05 |
| H3K27ac | H3K4me3 | 44.6350680 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom06 | Less than 0.05 |
| H3K27ac | H3K9ac | 35.4811627 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom06 | Less than 0.05 |
| H3K27ac | phH3_S10 | 59.7124355 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom06 | Less than 0.05 |
| H3K4me3 | H3K9ac | 9.1539053 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom06 | Less than 0.05 |
| H3K4me3 | phH3_S10 | 104.3475035 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom06 | Less than 0.05 |
| H3K9ac | phH3_S10 | 95.1935982 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom06 | Less than 0.05 |
| FxCycle | H3K14ac | 54.5220112 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom07 | Less than 0.05 |
| FxCycle | H3K27ac | 9.8274456 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom07 | Less than 0.05 |
| FxCycle | H3K4me3 | 58.9807580 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom07 | Less than 0.05 |
| FxCycle | H3K9ac | 34.4405247 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom07 | Less than 0.05 |
| FxCycle | phH3_S10 | 74.0701977 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom07 | Less than 0.05 |
| H3K14ac | H3K27ac | 44.6945657 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom07 | Less than 0.05 |
| H3K14ac | H3K4me3 | 113.5027693 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom07 | Less than 0.05 |
| H3K14ac | H3K9ac | 88.9625360 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom07 | Less than 0.05 |
| H3K14ac | phH3_S10 | 19.5481865 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom07 | Less than 0.05 |
| H3K27ac | H3K4me3 | 68.8082036 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom07 | Less than 0.05 |
| H3K27ac | H3K9ac | 44.2679703 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom07 | Less than 0.05 |
| H3K27ac | phH3_S10 | 64.2427522 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom07 | Less than 0.05 |
| H3K4me3 | H3K9ac | 24.5402333 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom07 | Less than 0.05 |
| H3K4me3 | phH3_S10 | 133.0509558 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom07 | Less than 0.05 |
| H3K9ac | phH3_S10 | 108.5107224 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom07 | Less than 0.05 |
| FxCycle | H3K14ac | 59.4461956 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom08 | Less than 0.05 |
| FxCycle | H3K27ac | 5.6822524 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom08 | Less than 0.05 |
| FxCycle | H3K4me3 | 71.3769273 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom08 | Less than 0.05 |
| FxCycle | H3K9ac | 46.4352272 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom08 | Less than 0.05 |
| FxCycle | phH3_S10 | 82.3953903 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom08 | Less than 0.05 |
| H3K14ac | H3K27ac | 53.7639432 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom08 | Less than 0.05 |
| H3K14ac | H3K4me3 | 130.8231229 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom08 | Less than 0.05 |
| H3K14ac | H3K9ac | 105.8814227 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom08 | Less than 0.05 |
| H3K14ac | phH3_S10 | 22.9491947 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom08 | Less than 0.05 |
| H3K27ac | H3K4me3 | 77.0591797 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom08 | Less than 0.05 |
| H3K27ac | H3K9ac | 52.1174796 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom08 | Less than 0.05 |
| H3K27ac | phH3_S10 | 76.7131379 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom08 | Less than 0.05 |
| H3K4me3 | H3K9ac | 24.9417001 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom08 | Less than 0.05 |
| H3K4me3 | phH3_S10 | 153.7723176 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom08 | Less than 0.05 |
| H3K9ac | phH3_S10 | 128.8306175 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom08 | Less than 0.05 |
| FxCycle | H3K14ac | 7.5565053 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom09 | Less than 0.05 |
| FxCycle | H3K27ac | 4.0070893 | 0.0001025 | two.sided | z | FDR | Dunn | list, it.... | fsom09 | Less than 0.05 |
| FxCycle | H3K4me3 | 3.8598344 | 0.0001702 | two.sided | z | FDR | Dunn | list, it.... | fsom09 | Less than 0.05 |
| FxCycle | H3K9ac | 2.0750306 | 0.0517959 | two.sided | z | FDR | Dunn | list, it.... | fsom09 | More than 0.05 |
| FxCycle | phH3_S10 | 6.2720014 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom09 | Less than 0.05 |
| H3K14ac | H3K27ac | 11.5635947 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom09 | Less than 0.05 |
| H3K14ac | H3K4me3 | 11.4163397 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom09 | Less than 0.05 |
| H3K14ac | H3K9ac | 9.6315360 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom09 | Less than 0.05 |
| H3K14ac | phH3_S10 | 1.2845039 | 0.2131775 | two.sided | z | FDR | Dunn | list, it.... | fsom09 | More than 0.05 |
| H3K27ac | H3K4me3 | 0.1472550 | 0.8829308 | two.sided | z | FDR | Dunn | list, it.... | fsom09 | More than 0.05 |
| H3K27ac | H3K9ac | 1.9320587 | 0.0666903 | two.sided | z | FDR | Dunn | list, it.... | fsom09 | More than 0.05 |
| H3K27ac | phH3_S10 | 10.2790907 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom09 | Less than 0.05 |
| H3K4me3 | H3K9ac | 1.7848037 | 0.0857229 | two.sided | z | FDR | Dunn | list, it.... | fsom09 | More than 0.05 |
| H3K4me3 | phH3_S10 | 10.1318358 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom09 | Less than 0.05 |
| H3K9ac | phH3_S10 | 8.3470320 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom09 | Less than 0.05 |
| FxCycle | H3K14ac | 13.8431454 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom10 | Less than 0.05 |
| FxCycle | H3K27ac | 3.4019654 | 0.0006690 | two.sided | z | FDR | Dunn | list, it.... | fsom10 | Less than 0.05 |
| FxCycle | H3K4me3 | 14.8753846 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom10 | Less than 0.05 |
| FxCycle | H3K9ac | 10.7653871 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom10 | Less than 0.05 |
| FxCycle | phH3_S10 | 9.3222544 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom10 | Less than 0.05 |
| H3K14ac | H3K27ac | 17.2451108 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom10 | Less than 0.05 |
| H3K14ac | H3K4me3 | 28.7185300 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom10 | Less than 0.05 |
| H3K14ac | H3K9ac | 24.6085325 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom10 | Less than 0.05 |
| H3K14ac | phH3_S10 | 4.5208910 | 0.0000071 | two.sided | z | FDR | Dunn | list, it.... | fsom10 | Less than 0.05 |
| H3K27ac | H3K4me3 | 11.4734191 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom10 | Less than 0.05 |
| H3K27ac | H3K9ac | 7.3634216 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom10 | Less than 0.05 |
| H3K27ac | phH3_S10 | 12.7242198 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom10 | Less than 0.05 |
| H3K4me3 | H3K9ac | 4.1099975 | 0.0000424 | two.sided | z | FDR | Dunn | list, it.... | fsom10 | Less than 0.05 |
| H3K4me3 | phH3_S10 | 24.1976390 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom10 | Less than 0.05 |
| H3K9ac | phH3_S10 | 20.0876415 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom10 | Less than 0.05 |
| FxCycle | H3K14ac | 35.3313215 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom11 | Less than 0.05 |
| FxCycle | H3K27ac | 12.9400152 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom11 | Less than 0.05 |
| FxCycle | H3K4me3 | 2.8404865 | 0.0051975 | two.sided | z | FDR | Dunn | list, it.... | fsom11 | Less than 0.05 |
| FxCycle | H3K9ac | 12.3781030 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom11 | Less than 0.05 |
| FxCycle | phH3_S10 | 33.9663401 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom11 | Less than 0.05 |
| H3K14ac | H3K27ac | 22.3913063 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom11 | Less than 0.05 |
| H3K14ac | H3K4me3 | 38.1718081 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom11 | Less than 0.05 |
| H3K14ac | H3K9ac | 22.9532185 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom11 | Less than 0.05 |
| H3K14ac | phH3_S10 | 1.3649814 | 0.1845631 | two.sided | z | FDR | Dunn | list, it.... | fsom11 | More than 0.05 |
| H3K27ac | H3K4me3 | 15.7805017 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom11 | Less than 0.05 |
| H3K27ac | H3K9ac | 0.5619122 | 0.5741759 | two.sided | z | FDR | Dunn | list, it.... | fsom11 | More than 0.05 |
| H3K27ac | phH3_S10 | 21.0263249 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom11 | Less than 0.05 |
| H3K4me3 | H3K9ac | 15.2185896 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom11 | Less than 0.05 |
| H3K4me3 | phH3_S10 | 36.8068266 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom11 | Less than 0.05 |
| H3K9ac | phH3_S10 | 21.5882371 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom11 | Less than 0.05 |
| FxCycle | H3K14ac | 11.3802378 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom12 | Less than 0.05 |
| FxCycle | H3K27ac | 3.1478817 | 0.0020557 | two.sided | z | FDR | Dunn | list, it.... | fsom12 | Less than 0.05 |
| FxCycle | H3K4me3 | 3.9710085 | 0.0000976 | two.sided | z | FDR | Dunn | list, it.... | fsom12 | Less than 0.05 |
| FxCycle | H3K9ac | 2.3224420 | 0.0233182 | two.sided | z | FDR | Dunn | list, it.... | fsom12 | Less than 0.05 |
| FxCycle | phH3_S10 | 13.2885314 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom12 | Less than 0.05 |
| H3K14ac | H3K27ac | 8.2323562 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom12 | Less than 0.05 |
| H3K14ac | H3K4me3 | 15.3512463 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom12 | Less than 0.05 |
| H3K14ac | H3K9ac | 13.7026798 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom12 | Less than 0.05 |
| H3K14ac | phH3_S10 | 1.9082936 | 0.0603785 | two.sided | z | FDR | Dunn | list, it.... | fsom12 | More than 0.05 |
| H3K27ac | H3K4me3 | 7.1188901 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom12 | Less than 0.05 |
| H3K27ac | H3K9ac | 5.4703237 | 0.0000001 | two.sided | z | FDR | Dunn | list, it.... | fsom12 | Less than 0.05 |
| H3K27ac | phH3_S10 | 10.1406497 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom12 | Less than 0.05 |
| H3K4me3 | H3K9ac | 1.6485665 | 0.0992365 | two.sided | z | FDR | Dunn | list, it.... | fsom12 | More than 0.05 |
| H3K4me3 | phH3_S10 | 17.2595399 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom12 | Less than 0.05 |
| H3K9ac | phH3_S10 | 15.6109734 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom12 | Less than 0.05 |
| FxCycle | H3K14ac | 15.7012151 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom13 | Less than 0.05 |
| FxCycle | H3K27ac | 3.0880772 | 0.0020146 | two.sided | z | FDR | Dunn | list, it.... | fsom13 | Less than 0.05 |
| FxCycle | H3K4me3 | 12.8561630 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom13 | Less than 0.05 |
| FxCycle | H3K9ac | 7.4377133 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom13 | Less than 0.05 |
| FxCycle | phH3_S10 | 20.1815381 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom13 | Less than 0.05 |
| H3K14ac | H3K27ac | 12.6131379 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom13 | Less than 0.05 |
| H3K14ac | H3K4me3 | 28.5573781 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom13 | Less than 0.05 |
| H3K14ac | H3K9ac | 23.1389284 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom13 | Less than 0.05 |
| H3K14ac | phH3_S10 | 4.4803230 | 0.0000080 | two.sided | z | FDR | Dunn | list, it.... | fsom13 | Less than 0.05 |
| H3K27ac | H3K4me3 | 15.9442402 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom13 | Less than 0.05 |
| H3K27ac | H3K9ac | 10.5257905 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom13 | Less than 0.05 |
| H3K27ac | phH3_S10 | 17.0934609 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom13 | Less than 0.05 |
| H3K4me3 | H3K9ac | 5.4184497 | 0.0000001 | two.sided | z | FDR | Dunn | list, it.... | fsom13 | Less than 0.05 |
| H3K4me3 | phH3_S10 | 33.0377011 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom13 | Less than 0.05 |
| H3K9ac | phH3_S10 | 27.6192514 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom13 | Less than 0.05 |
| FxCycle | H3K14ac | 12.7518756 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom14 | Less than 0.05 |
| FxCycle | H3K27ac | 4.8377864 | 0.0000015 | two.sided | z | FDR | Dunn | list, it.... | fsom14 | Less than 0.05 |
| FxCycle | H3K4me3 | 11.6365472 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom14 | Less than 0.05 |
| FxCycle | H3K9ac | 0.7063804 | 0.4799516 | two.sided | z | FDR | Dunn | list, it.... | fsom14 | More than 0.05 |
| FxCycle | phH3_S10 | 10.3938092 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom14 | Less than 0.05 |
| H3K14ac | H3K27ac | 7.9140893 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom14 | Less than 0.05 |
| H3K14ac | H3K4me3 | 24.3884228 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom14 | Less than 0.05 |
| H3K14ac | H3K9ac | 13.4582560 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom14 | Less than 0.05 |
| H3K14ac | phH3_S10 | 23.1456848 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom14 | Less than 0.05 |
| H3K27ac | H3K4me3 | 16.4743336 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom14 | Less than 0.05 |
| H3K27ac | H3K9ac | 5.5441667 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom14 | Less than 0.05 |
| H3K27ac | phH3_S10 | 15.2315955 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom14 | Less than 0.05 |
| H3K4me3 | H3K9ac | 10.9301668 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom14 | Less than 0.05 |
| H3K4me3 | phH3_S10 | 1.2427381 | 0.2292475 | two.sided | z | FDR | Dunn | list, it.... | fsom14 | More than 0.05 |
| H3K9ac | phH3_S10 | 9.6874288 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | fsom14 | Less than 0.05 |
Gating Strategies
Goal: Compare gating strategies to assess whether H3 biogenesis through cell cycle is driving differences in H3-PTMs
Data with manual gates * Gating strategy 1: NPC -> cell Cycle phase -> H3-PTM * Gating strategy 2: NPC -> cell Cycle phase -> Total H3 -> H3-PTM
Note
When exporting from OMIQ, it’s important to export data filter by filter so that no events are dropped.
| clusterid | feature | mfi | |
|---|---|---|---|
| Length:307341 | Length:307341 | Min. :-2.6612 | |
| Class :character | Class :character | 1st Qu.: 0.4556 | |
| Mode :character | Mode :character | Median : 2.6315 | |
| NA | NA | Mean : 2.4704 | |
| NA | NA | 3rd Qu.: 4.2856 | |
| NA | NA | Max. : 6.3811 |
| Var1 | Freq |
|---|---|
| NPC/G0_G1 | 114687 |
| NPC/G0_G1/H3 | 109413 |
| NPC/G2 | 41031 |
| NPC/G2/H3 | 39411 |
| NPC/M | 1422 |
| NPC/M/H3 | 1377 |
Note
Plots should be generated comparing cluster strategies on x, mfi values on y and one plot per feature.
Show code
generate_cluster_plots <- function(H3, output_dir) {
# Ensure the output directory exists
if (!dir.exists(output_dir)) {
dir.create(output_dir, recursive = TRUE)
}
# Use actual feature names from the data
feature_id <- unique(H3$feature)
# Create a list to hold the plots
plot_list_2 <- list()
# Loop over each feature and generate the plot
for (feature in feature_id) {
plot_2 <- H3 %>%
filter(feature == !!feature) %>%
ggbetweenstats(
x = clusterid,
y = mfi,
type = "np", # Non-parametric test
pairwise.display = "none", # Display only significant pairwise comparisons
p.adjust.method = "fdr",
p.value.args = list(digits = 4), # Adjust p-values for multiple tests using this method
results.subtitle = TRUE,
ggplot.component = list(
scale_color_manual(values = c("#b8553c","#46c19a","#b84c7d","#6da24d","#7f62b8","#bd9d3c")))
) +
# Add labels and title
labs(
x = "Gating Strategy",
y = "Fluorescence Intensity",
title = paste("Gating strategy comparison for:", feature)
) +
theme( # Customizations
text = element_text(family = "Times New Roman", size = 8, color = "black"),
plot.title = element_text(
family = "Times New Roman",
size = 12,
face = "bold",
color = "#2a475e"
),
plot.subtitle = element_text(
family = "Times New Roman",
size = 8,
face = "bold",
color = "#1b2838"
),
plot.title.position = "plot",
axis.text = element_text(size = 8, color = "black"),
axis.title = element_text(size = 8),
axis.ticks = element_blank(),
axis.line = element_line(colour = "grey50"),
panel.grid = element_line(color = "#b4aea9"),
panel.grid.minor = element_blank(),
panel.grid.major.x = element_blank(),
panel.grid.major.y = element_line(linetype = "dashed"),
panel.background = element_rect(fill = "white", color = "white"),
plot.background = element_rect(fill = "white", color = "white")
)
# Add the plot to a list
plot_list_2[[feature]] <- plot_2
# Save the individual plot as PNG
ggsave(
filename = file.path(output_dir, paste0("gate_h3_violin_plot_", feature, ".png")),
plot = plot_2,
width = 20, height = 12, units = "cm", dpi = 600
)
# Save the individual plot as SVG
ggsave(
filename = file.path(output_dir, paste0("gate_h3_violin_plot_", feature, ".svg")),
plot = plot_2,
width = 20, height = 12, units = "cm"
)
print(plot_2)
}
# Combine all plots into a grid with 5 rows (or adjust as needed)
combined_plot_2 <- wrap_plots(plot_list_2, nrow = 5)
# Save the combined plot as PNG
ggsave(
filename = file.path(output_dir, "combined_h3_gate_violin_plots.png"),
plot = combined_plot_2,
width = 40, height = 50, units = "cm", dpi = 600
)
# Save the combined plot as SVG
ggsave(
filename = file.path(output_dir, "combined_h3_gate_violin_plots.svg"),
plot = combined_plot_2,
width = 40, height = 50, units = "cm"
)
}
# Example usage:
output_directory <- "output/gate_violin_plots"
generate_cluster_plots(H3, output_directory)
Pairwise comparison stats
| group1 | group2 | statistic | p.value | alternative | distribution | p.adjust.method | test | expression | p_comparison |
|---|---|---|---|---|---|---|---|---|---|
| NPC/G0_G1 | NPC/G0_G1/H3 | 2.4827192 | 0.0217306 | two.sided | z | FDR | Dunn | list, it.... | Less than 0.05 |
| NPC/G2 | NPC/G2/H3 | 1.7416275 | 0.1223605 | two.sided | z | FDR | Dunn | list, it.... | More than 0.05 |
| NPC/M | NPC/M/H3 | 0.2029177 | 0.8391993 | two.sided | z | FDR | Dunn | list, it.... | More than 0.05 |
| group1 | group2 | statistic | p.value | alternative | distribution | p.adjust.method | test | expression | p_comparison |
|---|---|---|---|---|---|---|---|---|---|
| NPC/G0_G1 | NPC/G0_G1/H3 | 1.6052049 | 0.1161951 | two.sided | z | FDR | Dunn | list, it.... | More than 0.05 |
| NPC/G2 | NPC/G2/H3 | 1.9205789 | 0.0632133 | two.sided | z | FDR | Dunn | list, it.... | More than 0.05 |
| NPC/M | NPC/M/H3 | 0.0405092 | 0.9676872 | two.sided | z | FDR | Dunn | list, it.... | More than 0.05 |
| group1 | group2 | statistic | p.value | alternative | distribution | p.adjust.method | test | expression | p_comparison |
|---|---|---|---|---|---|---|---|---|---|
| NPC/G0_G1 | NPC/G0_G1/H3 | 2.3680538 | 0.0206330 | two.sided | z | FDR | Dunn | list, it.... | Less than 0.05 |
| NPC/G2 | NPC/G2/H3 | 2.2054539 | 0.0293810 | two.sided | z | FDR | Dunn | list, it.... | Less than 0.05 |
| NPC/M | NPC/M/H3 | 0.0157778 | 0.9874116 | two.sided | z | FDR | Dunn | list, it.... | More than 0.05 |
| group1 | group2 | statistic | p.value | alternative | distribution | p.adjust.method | test | expression | p_comparison |
|---|---|---|---|---|---|---|---|---|---|
| NPC/G0_G1 | NPC/G0_G1/H3 | 2.7161112 | 0.0076216 | two.sided | z | FDR | Dunn | list, it.... | Less than 0.05 |
| NPC/G2 | NPC/G2/H3 | 2.1447975 | 0.0342525 | two.sided | z | FDR | Dunn | list, it.... | Less than 0.05 |
| NPC/M | NPC/M/H3 | 0.1659177 | 0.8682217 | two.sided | z | FDR | Dunn | list, it.... | More than 0.05 |
| group1 | group2 | statistic | p.value | alternative | distribution | p.adjust.method | test | expression | p_comparison |
|---|---|---|---|---|---|---|---|---|---|
| NPC/G0_G1 | NPC/G0_G1/H3 | 1.3302952 | 0.2116397 | two.sided | z | FDR | Dunn | list, it.... | More than 0.05 |
| NPC/G2 | NPC/G2/H3 | 1.0306637 | 0.3243199 | two.sided | z | FDR | Dunn | list, it.... | More than 0.05 |
| NPC/M | NPC/M/H3 | 0.0828863 | 0.9339420 | two.sided | z | FDR | Dunn | list, it.... | More than 0.05 |
| group1 | group2 | statistic | p.value | alternative | distribution | p.adjust.method | test | expression | p_comparison |
|---|---|---|---|---|---|---|---|---|---|
| NPC/G0_G1 | NPC/G0_G1/H3 | 5.8202567 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Less than 0.05 |
| NPC/G2 | NPC/G2/H3 | 3.8681118 | 0.0001645 | two.sided | z | FDR | Dunn | list, it.... | Less than 0.05 |
| NPC/M | NPC/M/H3 | 0.5914249 | 0.6395028 | two.sided | z | FDR | Dunn | list, it.... | More than 0.05 |
| group1 | group2 | statistic | p.value | alternative | distribution | p.adjust.method | test | expression | p_comparison |
|---|---|---|---|---|---|---|---|---|---|
| NPC/G0_G1 | NPC/G0_G1/H3 | 2.668879 | 0.0087813 | two.sided | z | FDR | Dunn | list, it.... | Less than 0.05 |
| NPC/G2 | NPC/G2/H3 | 2.214119 | 0.0287364 | two.sided | z | FDR | Dunn | list, it.... | Less than 0.05 |
| NPC/M | NPC/M/H3 | 0.001559 | 0.9987561 | two.sided | z | FDR | Dunn | list, it.... | More than 0.05 |
| group1 | group2 | statistic | p.value | alternative | distribution | p.adjust.method | test | expression | p_comparison |
|---|---|---|---|---|---|---|---|---|---|
| NPC/G0_G1 | NPC/G0_G1/H3 | 1.4707876 | 0.2285327 | two.sided | z | FDR | Dunn | list, it.... | More than 0.05 |
| NPC/G2 | NPC/G2/H3 | 0.2724365 | 0.8413783 | two.sided | z | FDR | Dunn | list, it.... | More than 0.05 |
| NPC/M | NPC/M/H3 | 0.0210118 | 0.9832363 | two.sided | z | FDR | Dunn | list, it.... | More than 0.05 |
Drug treatments
Drug treatment assays to assess sensitivity of EpiFlow identification in both, spectral and conventional flow cytometry
Summary of spectral flow cytometry experiment
| Cell line | WTC11 |
| Differentiation | Neuronal progenitor cells (NPC) |
| Treatment 1 | DMSO control |
| Treatment 2 |
Trichostatin A (TSA) (0.5, 1 and 10 µM) HDAC inhibitor, showed to increase H3K27ac (PMID: 23093607). Expected outcome: increase in acetylation marks |
| Treatment 3 |
A-485 (1, 10 and 20 µM) p300/CBP inhibitor, showed to decrease H3K27ac (PMID: 28953875). Expected outcome: decreased acetylation marks. |
| Replicates | 3 biological replicates per experimental group |
| event | H3K9ac | H3K14ac | H3K4me1 | H3K27ac | gate | treatment |
|---|---|---|---|---|---|---|
| 4629 | 5.0134 | 0.532710 | 4.4401 | 6.4594 | Mitosis | DMSO |
| 4630 | 5.6764 | -0.039929 | 4.0351 | 6.4341 | G2 | DMSO |
| 4634 | 5.1459 | -0.059104 | 5.0237 | 6.8079 | G0/G1 | DMSO |
| 4635 | 5.2293 | 0.361370 | 5.6113 | 7.2979 | NPC | PAX6+ | DMSO |
| 4637 | 5.0843 | 0.049410 | 4.1713 | 6.5476 | Other | DMSO |
| 4638 | 5.3414 | 0.081570 | 4.2808 | 6.6148 | G0/G1 | DMSO |
| event | gate | treatment | feature | mfi |
|---|---|---|---|---|
| 4629 | Mitosis | DMSO | H3K9ac | 5.0134 |
| 4630 | G2 | DMSO | H3K9ac | 5.6764 |
| 4634 | G0/G1 | DMSO | H3K9ac | 5.1459 |
| 4635 | NPC | PAX6+ | DMSO | H3K9ac | 5.2293 |
| 4637 | Other | DMSO | H3K9ac | 5.0843 |
| 4638 | G0/G1 | DMSO | H3K9ac | 5.3414 |
| event | gate | treatment | feature | mfi | |
|---|---|---|---|---|---|
| Min. : 1112 | Length:1551252 | Length:1551252 | Length:1551252 | Min. :-3.924 | |
| 1st Qu.: 52931 | Class :character | Class :character | Class :character | 1st Qu.: 2.358 | |
| Median :100295 | Mode :character | Mode :character | Mode :character | Median : 4.597 | |
| Mean :120741 | NA | NA | NA | Mean : 4.063 | |
| 3rd Qu.:157830 | NA | NA | NA | 3rd Qu.: 5.816 | |
| Max. :583396 | NA | NA | NA | Max. : 7.609 |
| event | gate | treatment | feature | mfi | mfi_z.V1 | |
|---|---|---|---|---|---|---|
| Min. : 1112 | Length:1551252 | Length:1551252 | Length:1551252 | Min. :-3.924 | Min. :-3.601487 | |
| 1st Qu.: 52931 | Class :character | Class :character | Class :character | 1st Qu.: 2.358 | 1st Qu.:-0.768861 | |
| Median :100295 | Mode :character | Mode :character | Mode :character | Median : 4.597 | Median : 0.240759 | |
| Mean :120741 | NA | NA | NA | Mean : 4.063 | Mean : 0.000000 | |
| 3rd Qu.:157830 | NA | NA | NA | 3rd Qu.: 5.816 | 3rd Qu.: 0.790276 | |
| Max. :583396 | NA | NA | NA | Max. : 7.609 | Max. : 1.598658 |
| event | gate | treatment | feature | mfi | mfi_z |
|---|---|---|---|---|---|
| 4629 | Mitosis | DMSO | H3K9ac | 5.0134 | 0.4283355 |
| 4630 | G2 | DMSO | H3K9ac | 5.6764 | 0.7272851 |
| 4634 | G0/G1 | DMSO | H3K9ac | 5.1459 | 0.4880803 |
| 4635 | NPC | PAX6+ | DMSO | H3K9ac | 5.2293 | 0.5256857 |
| 4637 | Other | DMSO | H3K9ac | 5.0843 | 0.4603046 |
| 4638 | G0/G1 | DMSO | H3K9ac | 5.3414 | 0.5762321 |
Assess spectral flow sensitivity on fluorescent intensity values distributions per feature within each cell cycle phase
Assess spectral flow sensitivity on fluorescent intensity values distributions of all features within each cell cycle phase
Statistical analysis to assess the effect of drug treatments in each feature
Pairwise comparisons
Extracting pairwise comparisons
| group1 | group2 | statistic | p.value | alternative | distribution | p.adjust.method | test | expression | Gate | Feature | Significance |
|---|---|---|---|---|---|---|---|---|---|---|---|
| A485 10um | A485 20um | 0.9068690 | 0.3826999 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K9ac | More than 0.05 |
| A485 10um | TSA 05um | 84.8632708 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K9ac | Less than 0.05 |
| A485 10um | TSA 10um | 97.4909448 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K9ac | Less than 0.05 |
| A485 10um | TSA 1um | 81.5102892 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K9ac | Less than 0.05 |
| A485 1um | A485 10um | 16.8927188 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K9ac | Less than 0.05 |
| A485 1um | A485 20um | 16.5865824 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K9ac | Less than 0.05 |
| A485 1um | TSA 05um | 70.9631481 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K9ac | Less than 0.05 |
| A485 1um | TSA 10um | 80.5748676 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K9ac | Less than 0.05 |
| A485 1um | TSA 1um | 67.5962834 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K9ac | Less than 0.05 |
| A485 20um | TSA 05um | 85.3722052 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K9ac | Less than 0.05 |
| A485 20um | TSA 10um | 98.4496342 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K9ac | Less than 0.05 |
| A485 20um | TSA 1um | 81.9927977 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K9ac | Less than 0.05 |
| DMSO | A485 10um | 70.4285761 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K9ac | Less than 0.05 |
| DMSO | A485 1um | 43.1838364 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K9ac | Less than 0.05 |
| DMSO | A485 20um | 72.6809904 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K9ac | Less than 0.05 |
| DMSO | TSA 05um | 49.6393166 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K9ac | Less than 0.05 |
| DMSO | TSA 10um | 57.7421748 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K9ac | Less than 0.05 |
| DMSO | TSA 1um | 45.8513140 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K9ac | Less than 0.05 |
| TSA 05um | TSA 10um | 0.2048217 | 0.8377114 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K9ac | More than 0.05 |
| TSA 05um | TSA 1um | 3.2014716 | 0.0015112 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K9ac | Less than 0.05 |
| TSA 1um | TSA 10um | 3.6672221 | 0.0002861 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K9ac | Less than 0.05 |
| A485 10um | A485 20um | 2.5107497 | 0.0126499 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K27ac | Less than 0.05 |
| A485 10um | TSA 05um | 59.7950434 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K27ac | Less than 0.05 |
| A485 10um | TSA 10um | 63.1191182 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K27ac | Less than 0.05 |
| A485 10um | TSA 1um | 43.4845316 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K27ac | Less than 0.05 |
| A485 1um | A485 10um | 8.1836971 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K27ac | Less than 0.05 |
| A485 1um | A485 20um | 10.6480856 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K27ac | Less than 0.05 |
| A485 1um | TSA 05um | 62.4830194 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K27ac | Less than 0.05 |
| A485 1um | TSA 10um | 65.6138278 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K27ac | Less than 0.05 |
| A485 1um | TSA 1um | 46.8395016 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K27ac | Less than 0.05 |
| A485 20um | TSA 05um | 59.0986256 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K27ac | Less than 0.05 |
| A485 20um | TSA 10um | 62.4931032 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K27ac | Less than 0.05 |
| A485 20um | TSA 1um | 42.5884932 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K27ac | Less than 0.05 |
| DMSO | A485 10um | 84.2061306 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K27ac | Less than 0.05 |
| DMSO | A485 1um | 82.3460084 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K27ac | Less than 0.05 |
| DMSO | A485 20um | 85.3068318 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K27ac | Less than 0.05 |
| DMSO | TSA 05um | 16.3423420 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K27ac | Less than 0.05 |
| DMSO | TSA 10um | 13.3078276 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K27ac | Less than 0.05 |
| DMSO | TSA 1um | 0.9175614 | 0.3588486 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K27ac | More than 0.05 |
| TSA 05um | TSA 10um | 3.9268720 | 0.0000951 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K27ac | Less than 0.05 |
| TSA 05um | TSA 1um | 13.0209436 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K27ac | Less than 0.05 |
| TSA 1um | TSA 10um | 10.1242249 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K27ac | Less than 0.05 |
| A485 10um | A485 20um | 2.3413153 | 0.0201767 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K14ac | Less than 0.05 |
| A485 10um | TSA 05um | 62.7634521 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K14ac | Less than 0.05 |
| A485 10um | TSA 10um | 78.6647860 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K14ac | Less than 0.05 |
| A485 10um | TSA 1um | 66.0529693 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K14ac | Less than 0.05 |
| A485 1um | A485 10um | 17.4779823 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K14ac | Less than 0.05 |
| A485 1um | A485 20um | 15.9186700 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K14ac | Less than 0.05 |
| A485 1um | TSA 05um | 49.3857457 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K14ac | Less than 0.05 |
| A485 1um | TSA 10um | 62.3096228 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K14ac | Less than 0.05 |
| A485 1um | TSA 1um | 52.4028698 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K14ac | Less than 0.05 |
| A485 20um | TSA 05um | 62.1982169 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K14ac | Less than 0.05 |
| A485 20um | TSA 10um | 78.3951737 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K14ac | Less than 0.05 |
| A485 20um | TSA 1um | 65.5298308 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K14ac | Less than 0.05 |
| DMSO | A485 10um | 31.0331017 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K14ac | Less than 0.05 |
| DMSO | A485 1um | 45.9985348 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K14ac | Less than 0.05 |
| DMSO | A485 20um | 35.0852026 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K14ac | Less than 0.05 |
| DMSO | TSA 05um | 81.5004685 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K14ac | Less than 0.05 |
| DMSO | TSA 10um | 101.3832420 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K14ac | Less than 0.05 |
| DMSO | TSA 1um | 85.1045584 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K14ac | Less than 0.05 |
| TSA 05um | TSA 10um | 4.9448644 | 0.0000009 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K14ac | Less than 0.05 |
| TSA 05um | TSA 1um | 2.0850595 | 0.0370639 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K14ac | Less than 0.05 |
| TSA 1um | TSA 10um | 2.7230357 | 0.0071494 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K14ac | Less than 0.05 |
| A485 10um | A485 20um | 0.1215996 | 0.9032161 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K4me1 | More than 0.05 |
| A485 10um | TSA 05um | 21.7737091 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K4me1 | Less than 0.05 |
| A485 10um | TSA 10um | 32.7407811 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K4me1 | Less than 0.05 |
| A485 10um | TSA 1um | 18.8380361 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K4me1 | Less than 0.05 |
| A485 1um | A485 10um | 7.9166609 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K4me1 | Less than 0.05 |
| A485 1um | A485 20um | 8.0418925 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K4me1 | Less than 0.05 |
| A485 1um | TSA 05um | 25.8202400 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K4me1 | Less than 0.05 |
| A485 1um | TSA 10um | 36.6169540 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K4me1 | Less than 0.05 |
| A485 1um | TSA 1um | 23.0313347 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K4me1 | Less than 0.05 |
| A485 20um | TSA 05um | 22.1039766 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K4me1 | Less than 0.05 |
| A485 20um | TSA 10um | 33.3389369 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K4me1 | Less than 0.05 |
| A485 20um | TSA 1um | 19.1380148 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K4me1 | Less than 0.05 |
| DMSO | A485 10um | 28.0884853 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K4me1 | Less than 0.05 |
| DMSO | A485 1um | 15.9462393 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K4me1 | Less than 0.05 |
| DMSO | A485 20um | 29.2547939 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K4me1 | Less than 0.05 |
| DMSO | TSA 05um | 37.6078279 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K4me1 | Less than 0.05 |
| DMSO | TSA 10um | 51.6579853 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K4me1 | Less than 0.05 |
| DMSO | TSA 1um | 34.7410197 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K4me1 | Less than 0.05 |
| TSA 05um | TSA 10um | 5.6969380 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K4me1 | Less than 0.05 |
| TSA 05um | TSA 1um | 2.4232140 | 0.0161531 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K4me1 | Less than 0.05 |
| TSA 1um | TSA 10um | 8.3538479 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G0/G1 | H3K4me1 | Less than 0.05 |
| A485 10um | A485 20um | 2.7941016 | 0.0060718 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K9ac | Less than 0.05 |
| A485 10um | TSA 05um | 80.8658363 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K9ac | Less than 0.05 |
| A485 10um | TSA 10um | 76.2856727 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K9ac | Less than 0.05 |
| A485 10um | TSA 1um | 42.2086798 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K9ac | Less than 0.05 |
| A485 1um | A485 10um | 1.8455858 | 0.0717895 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K9ac | More than 0.05 |
| A485 1um | A485 20um | 0.5609244 | 0.5748490 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K9ac | More than 0.05 |
| A485 1um | TSA 05um | 76.5209725 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K9ac | Less than 0.05 |
| A485 1um | TSA 10um | 72.6200827 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K9ac | Less than 0.05 |
| A485 1um | TSA 1um | 41.9331606 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K9ac | Less than 0.05 |
| A485 20um | TSA 05um | 85.1884288 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K9ac | Less than 0.05 |
| A485 20um | TSA 10um | 80.2247494 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K9ac | Less than 0.05 |
| A485 20um | TSA 1um | 43.9638737 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K9ac | Less than 0.05 |
| DMSO | A485 10um | 15.3429667 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K9ac | Less than 0.05 |
| DMSO | A485 1um | 15.3199167 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K9ac | Less than 0.05 |
| DMSO | A485 20um | 19.4421610 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K9ac | Less than 0.05 |
| DMSO | TSA 05um | 75.8700494 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K9ac | Less than 0.05 |
| DMSO | TSA 10um | 70.9128563 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K9ac | Less than 0.05 |
| DMSO | TSA 1um | 36.6019697 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K9ac | Less than 0.05 |
| TSA 05um | TSA 10um | 1.0901065 | 0.2894495 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K9ac | More than 0.05 |
| TSA 05um | TSA 1um | 7.5187483 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K9ac | Less than 0.05 |
| TSA 1um | TSA 10um | 6.6562721 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K9ac | Less than 0.05 |
| A485 10um | A485 20um | 1.1090017 | 0.2674294 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K27ac | More than 0.05 |
| A485 10um | TSA 05um | 35.5181571 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K27ac | Less than 0.05 |
| A485 10um | TSA 10um | 28.5173232 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K27ac | Less than 0.05 |
| A485 10um | TSA 1um | 15.7820135 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K27ac | Less than 0.05 |
| A485 1um | A485 10um | 9.7870612 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K27ac | Less than 0.05 |
| A485 1um | A485 20um | 9.1375046 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K27ac | Less than 0.05 |
| A485 1um | TSA 05um | 41.0208833 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K27ac | Less than 0.05 |
| A485 1um | TSA 10um | 34.3904411 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K27ac | Less than 0.05 |
| A485 1um | TSA 1um | 20.5600667 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K27ac | Less than 0.05 |
| A485 20um | TSA 05um | 37.3243963 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K27ac | Less than 0.05 |
| A485 20um | TSA 10um | 30.0380480 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K27ac | Less than 0.05 |
| A485 20um | TSA 1um | 16.4689799 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K27ac | Less than 0.05 |
| DMSO | A485 10um | 73.6149740 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K27ac | Less than 0.05 |
| DMSO | A485 1um | 74.5350534 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K27ac | Less than 0.05 |
| DMSO | A485 20um | 79.0879659 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K27ac | Less than 0.05 |
| DMSO | TSA 05um | 17.0497707 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K27ac | Less than 0.05 |
| DMSO | TSA 10um | 22.1933025 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K27ac | Less than 0.05 |
| DMSO | TSA 1um | 16.5547882 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K27ac | Less than 0.05 |
| TSA 05um | TSA 10um | 4.7881325 | 0.0000019 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K27ac | Less than 0.05 |
| TSA 05um | TSA 1um | 5.8813146 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K27ac | Less than 0.05 |
| TSA 1um | TSA 10um | 2.4850885 | 0.0135995 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K27ac | Less than 0.05 |
| A485 10um | A485 20um | 3.2808226 | 0.0010868 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K14ac | Less than 0.05 |
| A485 10um | TSA 05um | 68.7503326 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K14ac | Less than 0.05 |
| A485 10um | TSA 10um | 73.8328384 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K14ac | Less than 0.05 |
| A485 10um | TSA 1um | 43.7789647 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K14ac | Less than 0.05 |
| A485 1um | A485 10um | 8.0281691 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K14ac | Less than 0.05 |
| A485 1um | A485 20um | 5.4002772 | 0.0000001 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K14ac | Less than 0.05 |
| A485 1um | TSA 05um | 57.1327854 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K14ac | Less than 0.05 |
| A485 1um | TSA 10um | 62.4705962 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K14ac | Less than 0.05 |
| A485 1um | TSA 1um | 38.1585026 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K14ac | Less than 0.05 |
| A485 20um | TSA 05um | 68.0075270 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K14ac | Less than 0.05 |
| A485 20um | TSA 10um | 73.1721343 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K14ac | Less than 0.05 |
| A485 20um | TSA 1um | 42.6490086 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K14ac | Less than 0.05 |
| DMSO | A485 10um | 51.1876064 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K14ac | Less than 0.05 |
| DMSO | A485 1um | 53.1796337 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K14ac | Less than 0.05 |
| DMSO | A485 20um | 57.8902160 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K14ac | Less than 0.05 |
| DMSO | TSA 05um | 112.8850227 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K14ac | Less than 0.05 |
| DMSO | TSA 10um | 116.0131946 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K14ac | Less than 0.05 |
| DMSO | TSA 1um | 67.8580266 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K14ac | Less than 0.05 |
| TSA 05um | TSA 10um | 6.8265969 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K14ac | Less than 0.05 |
| TSA 05um | TSA 1um | 0.9918210 | 0.3212849 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K14ac | More than 0.05 |
| TSA 1um | TSA 10um | 3.7434969 | 0.0002006 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K14ac | Less than 0.05 |
| A485 10um | A485 20um | 2.7947569 | 0.0064160 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K4me1 | Less than 0.05 |
| A485 10um | TSA 05um | 4.0013140 | 0.0000882 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K4me1 | Less than 0.05 |
| A485 10um | TSA 10um | 7.1180601 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K4me1 | Less than 0.05 |
| A485 10um | TSA 1um | 1.9122012 | 0.0558504 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K4me1 | More than 0.05 |
| A485 1um | A485 10um | 15.9111363 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K4me1 | Less than 0.05 |
| A485 1um | A485 20um | 13.9787850 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K4me1 | Less than 0.05 |
| A485 1um | TSA 05um | 9.4255615 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K4me1 | Less than 0.05 |
| A485 1um | TSA 10um | 19.3078106 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K4me1 | Less than 0.05 |
| A485 1um | TSA 1um | 10.3921201 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K4me1 | Less than 0.05 |
| A485 20um | TSA 05um | 1.9244126 | 0.0558504 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K4me1 | More than 0.05 |
| A485 20um | TSA 10um | 9.3794993 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K4me1 | Less than 0.05 |
| A485 20um | TSA 1um | 3.2657866 | 0.0014327 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K4me1 | Less than 0.05 |
| DMSO | A485 10um | 17.6451259 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K4me1 | Less than 0.05 |
| DMSO | A485 1um | 2.3240559 | 0.0222407 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K4me1 | Less than 0.05 |
| DMSO | A485 20um | 15.4240555 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K4me1 | Less than 0.05 |
| DMSO | TSA 05um | 8.9650477 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K4me1 | Less than 0.05 |
| DMSO | TSA 10um | 20.3039223 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K4me1 | Less than 0.05 |
| DMSO | TSA 1um | 9.8289538 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K4me1 | Less than 0.05 |
| TSA 05um | TSA 10um | 9.4625039 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K4me1 | Less than 0.05 |
| TSA 05um | TSA 1um | 4.1142947 | 0.0000583 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K4me1 | Less than 0.05 |
| TSA 1um | TSA 10um | 2.4890094 | 0.0149449 | two.sided | z | FDR | Dunn | list, it.... | G2 | H3K4me1 | Less than 0.05 |
| A485 10um | A485 20um | 0.8281081 | 0.4755442 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K9ac | More than 0.05 |
| A485 10um | TSA 05um | 20.7816672 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K9ac | Less than 0.05 |
| A485 10um | TSA 10um | 20.4472298 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K9ac | Less than 0.05 |
| A485 10um | TSA 1um | 12.7478251 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K9ac | Less than 0.05 |
| A485 1um | A485 10um | 2.0665207 | 0.0479039 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K9ac | Less than 0.05 |
| A485 1um | A485 20um | 2.7897783 | 0.0069227 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K9ac | Less than 0.05 |
| A485 1um | TSA 05um | 17.6993755 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K9ac | Less than 0.05 |
| A485 1um | TSA 10um | 17.4986960 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K9ac | Less than 0.05 |
| A485 1um | TSA 1um | 11.3546642 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K9ac | Less than 0.05 |
| A485 20um | TSA 05um | 21.3701578 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K9ac | Less than 0.05 |
| A485 20um | TSA 10um | 21.0200700 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K9ac | Less than 0.05 |
| A485 20um | TSA 1um | 13.1147304 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K9ac | Less than 0.05 |
| DMSO | A485 10um | 13.6158817 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K9ac | Less than 0.05 |
| DMSO | A485 1um | 9.7005212 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K9ac | Less than 0.05 |
| DMSO | A485 20um | 14.4556219 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K9ac | Less than 0.05 |
| DMSO | TSA 05um | 11.4334613 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K9ac | Less than 0.05 |
| DMSO | TSA 10um | 11.3496749 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K9ac | Less than 0.05 |
| DMSO | TSA 1um | 6.9223700 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K9ac | Less than 0.05 |
| TSA 05um | TSA 10um | 0.1978983 | 0.9133112 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K9ac | More than 0.05 |
| TSA 05um | TSA 1um | 0.0267498 | 0.9786593 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K9ac | More than 0.05 |
| TSA 1um | TSA 10um | 0.1638869 | 0.9133112 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K9ac | More than 0.05 |
| A485 10um | A485 20um | 0.0809882 | 0.9354513 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K27ac | More than 0.05 |
| A485 10um | TSA 05um | 17.3792701 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K27ac | Less than 0.05 |
| A485 10um | TSA 10um | 18.1014039 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K27ac | Less than 0.05 |
| A485 10um | TSA 1um | 11.0507137 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K27ac | Less than 0.05 |
| A485 1um | A485 10um | 2.5924872 | 0.0125061 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K27ac | Less than 0.05 |
| A485 1um | A485 20um | 2.5192252 | 0.0145287 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K27ac | Less than 0.05 |
| A485 1um | TSA 05um | 18.1269990 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K27ac | Less than 0.05 |
| A485 1um | TSA 10um | 18.8132111 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K27ac | Less than 0.05 |
| A485 1um | TSA 1um | 12.0129442 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K27ac | Less than 0.05 |
| A485 20um | TSA 05um | 17.4272753 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K27ac | Less than 0.05 |
| A485 20um | TSA 10um | 18.1479528 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K27ac | Less than 0.05 |
| A485 20um | TSA 1um | 11.0842897 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K27ac | Less than 0.05 |
| DMSO | A485 10um | 14.9100006 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K27ac | Less than 0.05 |
| DMSO | A485 1um | 15.6062333 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K27ac | Less than 0.05 |
| DMSO | A485 20um | 14.9749688 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K27ac | Less than 0.05 |
| DMSO | TSA 05um | 7.0460692 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K27ac | Less than 0.05 |
| DMSO | TSA 10um | 8.0664961 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K27ac | Less than 0.05 |
| DMSO | TSA 1um | 4.6521762 | 0.0000046 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K27ac | Less than 0.05 |
| TSA 05um | TSA 10um | 0.9982009 | 0.3712123 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K27ac | More than 0.05 |
| TSA 05um | TSA 1um | 0.3368080 | 0.7730747 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K27ac | More than 0.05 |
| TSA 1um | TSA 10um | 0.3591996 | 0.7730747 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K27ac | More than 0.05 |
| A485 10um | A485 20um | 0.1306105 | 0.8960834 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K14ac | More than 0.05 |
| A485 10um | TSA 05um | 16.0305338 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K14ac | Less than 0.05 |
| A485 10um | TSA 10um | 16.5993265 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K14ac | Less than 0.05 |
| A485 10um | TSA 1um | 10.0133440 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K14ac | Less than 0.05 |
| A485 1um | A485 10um | 1.4495559 | 0.1931769 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K14ac | More than 0.05 |
| A485 1um | A485 20um | 1.3338764 | 0.2251254 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K14ac | More than 0.05 |
| A485 1um | TSA 05um | 13.7641443 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K14ac | Less than 0.05 |
| A485 1um | TSA 10um | 14.3770130 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K14ac | Less than 0.05 |
| A485 1um | TSA 1um | 9.0049936 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K14ac | Less than 0.05 |
| A485 20um | TSA 05um | 15.9257028 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K14ac | Less than 0.05 |
| A485 20um | TSA 10um | 16.4973125 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K14ac | Less than 0.05 |
| A485 20um | TSA 1um | 9.9526456 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K14ac | Less than 0.05 |
| DMSO | A485 10um | 9.2442460 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K14ac | Less than 0.05 |
| DMSO | A485 1um | 9.5139485 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K14ac | Less than 0.05 |
| DMSO | A485 20um | 9.3677237 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K14ac | Less than 0.05 |
| DMSO | TSA 05um | 22.9181571 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K14ac | Less than 0.05 |
| DMSO | TSA 10um | 23.2924251 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K14ac | Less than 0.05 |
| DMSO | TSA 1um | 14.0929571 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K14ac | Less than 0.05 |
| TSA 05um | TSA 10um | 0.8398602 | 0.4678179 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K14ac | More than 0.05 |
| TSA 05um | TSA 1um | 0.1450990 | 0.8960834 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K14ac | More than 0.05 |
| TSA 1um | TSA 10um | 0.4392470 | 0.7300071 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K14ac | More than 0.05 |
| A485 10um | A485 20um | 0.9845308 | 0.3590498 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K4me1 | More than 0.05 |
| A485 10um | TSA 05um | 0.4190263 | 0.7089567 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K4me1 | More than 0.05 |
| A485 10um | TSA 10um | 3.2030658 | 0.0031727 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K4me1 | Less than 0.05 |
| A485 10um | TSA 1um | 2.1622795 | 0.0494253 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K4me1 | Less than 0.05 |
| A485 1um | A485 10um | 2.0794499 | 0.0563640 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K4me1 | More than 0.05 |
| A485 1um | A485 20um | 1.2154713 | 0.2769361 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K4me1 | More than 0.05 |
| A485 1um | TSA 05um | 1.9893842 | 0.0653223 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K4me1 | More than 0.05 |
| A485 1um | TSA 10um | 4.5466120 | 0.0000164 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K4me1 | Less than 0.05 |
| A485 1um | TSA 1um | 3.1287494 | 0.0036866 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K4me1 | Less than 0.05 |
| A485 20um | TSA 05um | 1.1337897 | 0.2996966 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K4me1 | More than 0.05 |
| A485 20um | TSA 10um | 3.8965300 | 0.0002561 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K4me1 | Less than 0.05 |
| A485 20um | TSA 1um | 2.6015480 | 0.0177171 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K4me1 | Less than 0.05 |
| DMSO | A485 10um | 11.4426125 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K4me1 | Less than 0.05 |
| DMSO | A485 1um | 7.8003634 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K4me1 | Less than 0.05 |
| DMSO | A485 20um | 10.4093383 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K4me1 | Less than 0.05 |
| DMSO | TSA 05um | 8.5960468 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K4me1 | Less than 0.05 |
| DMSO | TSA 10um | 11.1939693 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K4me1 | Less than 0.05 |
| DMSO | TSA 1um | 7.1438052 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K4me1 | Less than 0.05 |
| TSA 05um | TSA 10um | 2.3236686 | 0.0352507 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K4me1 | Less than 0.05 |
| TSA 05um | TSA 1um | 1.7542374 | 0.1041992 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K4me1 | More than 0.05 |
| TSA 1um | TSA 10um | 0.1252149 | 0.9003534 | two.sided | z | FDR | Dunn | list, it.... | Mitosis | H3K4me1 | More than 0.05 |
| A485 10um | A485 20um | 2.8147764 | 0.0048811 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K9ac | Less than 0.05 |
| A485 10um | TSA 05um | 248.0654870 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K9ac | Less than 0.05 |
| A485 10um | TSA 10um | 256.4649292 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K9ac | Less than 0.05 |
| A485 10um | TSA 1um | 190.1380387 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K9ac | Less than 0.05 |
| A485 1um | A485 10um | 9.1750964 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K9ac | Less than 0.05 |
| A485 1um | A485 20um | 11.8753846 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K9ac | Less than 0.05 |
| A485 1um | TSA 05um | 248.5889284 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K9ac | Less than 0.05 |
| A485 1um | TSA 10um | 257.3213267 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K9ac | Less than 0.05 |
| A485 1um | TSA 1um | 188.3156788 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K9ac | Less than 0.05 |
| A485 20um | TSA 05um | 244.9928702 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K9ac | Less than 0.05 |
| A485 20um | TSA 10um | 253.2004264 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K9ac | Less than 0.05 |
| A485 20um | TSA 1um | 188.4114706 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K9ac | Less than 0.05 |
| DMSO | A485 10um | 27.6360927 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K9ac | Less than 0.05 |
| DMSO | A485 1um | 22.0432629 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K9ac | Less than 0.05 |
| DMSO | A485 20um | 29.2732910 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K9ac | Less than 0.05 |
| DMSO | TSA 05um | 132.0881705 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K9ac | Less than 0.05 |
| DMSO | TSA 10um | 137.6807469 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K9ac | Less than 0.05 |
| DMSO | TSA 1um | 93.6639148 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K9ac | Less than 0.05 |
| TSA 05um | TSA 10um | 9.4243870 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K9ac | Less than 0.05 |
| TSA 05um | TSA 1um | 65.4839154 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K9ac | Less than 0.05 |
| TSA 1um | TSA 10um | 74.9189919 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K9ac | Less than 0.05 |
| A485 10um | A485 20um | 4.6454246 | 0.0000034 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K27ac | Less than 0.05 |
| A485 10um | TSA 05um | 161.2479719 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K27ac | Less than 0.05 |
| A485 10um | TSA 10um | 170.5619304 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K27ac | Less than 0.05 |
| A485 10um | TSA 1um | 121.2202114 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K27ac | Less than 0.05 |
| A485 1um | A485 10um | 26.1926639 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K27ac | Less than 0.05 |
| A485 1um | A485 20um | 20.7789244 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K27ac | Less than 0.05 |
| A485 1um | TSA 05um | 196.0399199 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K27ac | Less than 0.05 |
| A485 1um | TSA 10um | 205.6761861 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K27ac | Less than 0.05 |
| A485 1um | TSA 1um | 154.8119501 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K27ac | Less than 0.05 |
| A485 20um | TSA 05um | 162.2434280 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K27ac | Less than 0.05 |
| A485 20um | TSA 10um | 171.3345497 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K27ac | Less than 0.05 |
| A485 20um | TSA 1um | 123.1823204 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K27ac | Less than 0.05 |
| DMSO | A485 10um | 82.4780185 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K27ac | Less than 0.05 |
| DMSO | A485 1um | 101.0134757 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K27ac | Less than 0.05 |
| DMSO | A485 20um | 84.8150179 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K27ac | Less than 0.05 |
| DMSO | TSA 05um | 19.5322093 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K27ac | Less than 0.05 |
| DMSO | TSA 10um | 25.7038135 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K27ac | Less than 0.05 |
| DMSO | TSA 1um | 7.2829333 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K27ac | Less than 0.05 |
| TSA 05um | TSA 10um | 10.2720378 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K27ac | Less than 0.05 |
| TSA 05um | TSA 1um | 45.1245756 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K27ac | Less than 0.05 |
| TSA 1um | TSA 10um | 55.4537142 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K27ac | Less than 0.05 |
| A485 10um | A485 20um | 5.4404104 | 0.0000001 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K14ac | Less than 0.05 |
| A485 10um | TSA 05um | 244.2574564 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K14ac | Less than 0.05 |
| A485 10um | TSA 10um | 292.5023610 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K14ac | Less than 0.05 |
| A485 10um | TSA 1um | 261.8417879 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K14ac | Less than 0.05 |
| A485 1um | A485 10um | 28.2700552 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K14ac | Less than 0.05 |
| A485 1um | A485 20um | 21.9855433 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K14ac | Less than 0.05 |
| A485 1um | TSA 05um | 224.1641975 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K14ac | Less than 0.05 |
| A485 1um | TSA 10um | 274.4327580 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K14ac | Less than 0.05 |
| A485 1um | TSA 1um | 242.3742550 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K14ac | Less than 0.05 |
| A485 20um | TSA 05um | 232.5039214 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K14ac | Less than 0.05 |
| A485 20um | TSA 10um | 279.5975083 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K14ac | Less than 0.05 |
| A485 20um | TSA 1um | 249.4547336 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K14ac | Less than 0.05 |
| DMSO | A485 10um | 21.3916080 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K14ac | Less than 0.05 |
| DMSO | A485 1um | 40.3204100 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K14ac | Less than 0.05 |
| DMSO | A485 20um | 24.8730148 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K14ac | Less than 0.05 |
| DMSO | TSA 05um | 180.0306060 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K14ac | Less than 0.05 |
| DMSO | TSA 10um | 211.3926484 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K14ac | Less than 0.05 |
| DMSO | TSA 1um | 190.3955041 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K14ac | Less than 0.05 |
| TSA 05um | TSA 10um | 52.2810563 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K14ac | Less than 0.05 |
| TSA 05um | TSA 1um | 15.9581817 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K14ac | Less than 0.05 |
| TSA 1um | TSA 10um | 37.0387938 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K14ac | Less than 0.05 |
| A485 10um | A485 20um | 2.7389044 | 0.0068133 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K4me1 | Less than 0.05 |
| A485 10um | TSA 05um | 2.6635541 | 0.0081186 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K4me1 | Less than 0.05 |
| A485 10um | TSA 10um | 20.1956815 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K4me1 | Less than 0.05 |
| A485 10um | TSA 1um | 34.7942936 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K4me1 | Less than 0.05 |
| A485 1um | A485 10um | 30.0320374 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K4me1 | Less than 0.05 |
| A485 1um | A485 20um | 26.5022777 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K4me1 | Less than 0.05 |
| A485 1um | TSA 05um | 29.4007036 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K4me1 | Less than 0.05 |
| A485 1um | TSA 10um | 53.1605103 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K4me1 | Less than 0.05 |
| A485 1um | TSA 1um | 3.7085167 | 0.0002736 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K4me1 | Less than 0.05 |
| A485 20um | TSA 05um | 0.3125997 | 0.7545848 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K4me1 | More than 0.05 |
| A485 20um | TSA 10um | 22.6103581 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K4me1 | Less than 0.05 |
| A485 20um | TSA 1um | 30.9824122 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K4me1 | Less than 0.05 |
| DMSO | A485 10um | 4.8444795 | 0.0000018 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K4me1 | Less than 0.05 |
| DMSO | A485 1um | 14.8251483 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K4me1 | Less than 0.05 |
| DMSO | A485 20um | 2.9372381 | 0.0038634 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K4me1 | Less than 0.05 |
| DMSO | TSA 05um | 3.2573467 | 0.0013892 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K4me1 | Less than 0.05 |
| DMSO | TSA 10um | 18.0555813 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K4me1 | Less than 0.05 |
| DMSO | TSA 1um | 17.3598197 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K4me1 | Less than 0.05 |
| TSA 05um | TSA 10um | 24.5860062 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K4me1 | Less than 0.05 |
| TSA 05um | TSA 1um | 34.6015773 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K4me1 | Less than 0.05 |
| TSA 1um | TSA 10um | 59.4513501 | 0.0000000 | two.sided | z | FDR | Dunn | list, it.... | Other | H3K4me1 | Less than 0.05 |
Show code
R version 4.4.1 (2024-06-14)
Platform: aarch64-apple-darwin20
Running under: macOS Ventura 13.2.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] grid stats graphics grDevices datasets utils methods
[8] base
other attached packages:
[1] colorRamp2_0.1.0 statsExpressions_1.5.5 kableExtra_1.4.0
[4] patchwork_1.2.0 ggstatsplot_0.12.4 ggpubr_0.6.0
[7] stringr_1.5.1 xml2_1.3.6 downlit_0.4.4
[10] svglite_2.1.3 Cairo_1.6-2 circlize_0.4.16
[13] ggridges_0.5.6 wesanderson_0.3.7 dendextend_1.17.1
[16] ComplexHeatmap_2.20.0 heatmaply_1.5.0 plotly_4.10.4
[19] hrbrthemes_0.8.7 seriation_1.5.5 dendsort_0.3.4
[22] readr_2.1.5 tidyr_1.3.1 ggExtra_0.10.1
[25] lubridate_1.9.3 viridis_0.6.5 viridisLite_0.4.2
[28] dplyr_1.1.4 ggplot2_3.5.1
loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 rstudioapi_0.16.0 jsonlite_1.8.8
[4] shape_1.4.6.1 datawizard_0.12.2 correlation_0.8.5
[7] magrittr_2.0.3 SuppDists_1.1-9.7 farver_2.1.2
[10] rmarkdown_2.27 GlobalOptions_0.1.2 vctrs_0.6.5
[13] memoise_2.0.1 paletteer_1.6.0 effectsize_0.8.9
[16] rstatix_0.7.2 webshot_0.5.5 htmltools_0.5.8.1
[19] curl_5.2.1 broom_1.0.6 BWStest_0.2.3
[22] htmlwidgets_1.6.4 cachem_1.1.0 mime_0.12
[25] lifecycle_1.0.4 iterators_1.0.14 pkgconfig_2.0.3
[28] R6_2.5.1 fastmap_1.2.0 PMCMRplus_1.9.10
[31] shiny_1.9.0 clue_0.3-65 digest_0.6.36
[34] colorspace_2.1-1 rematch2_2.1.2 S4Vectors_0.42.1
[37] crosstalk_1.2.1 labeling_0.4.3 fansi_1.0.6
[40] timechange_0.3.0 httr_1.4.7 abind_1.4-5
[43] compiler_4.4.1 bit64_4.0.5 fontquiver_0.2.1
[46] withr_3.0.0 doParallel_1.0.17 backports_1.5.0
[49] carData_3.0-5 highr_0.11 Rttf2pt1_1.3.12
[52] ggsignif_0.6.4 MASS_7.3-61 rjson_0.2.21
[55] gfonts_0.2.0 tools_4.4.1 httpuv_1.6.15
[58] extrafontdb_1.0 glue_1.7.0 promises_1.3.0
[61] cluster_2.1.6 generics_0.1.3 gtable_0.3.5
[64] tzdb_0.4.0 ca_0.71.1 data.table_1.15.4
[67] hms_1.1.3 car_3.1-2 utf8_1.2.4
[70] BiocGenerics_0.50.0 ggrepel_0.9.5 foreach_1.5.2
[73] pillar_1.9.0 vroom_1.6.5 later_1.3.2
[76] gmp_0.7-4 bit_4.0.5 renv_1.0.7
[79] tidyselect_1.2.1 registry_0.5-1 fontLiberation_0.1.0
[82] miniUI_0.1.1.1 knitr_1.48 fontBitstreamVera_0.1.1
[85] gridExtra_2.3 IRanges_2.38.1 crul_1.5.0
[88] stats4_4.4.1 xfun_0.46 matrixStats_1.3.0
[91] stringi_1.8.4 boot_1.3-30 lazyeval_0.2.2
[94] yaml_2.3.10 kSamples_1.2-10 evaluate_0.24.0
[97] codetools_0.2-20 httpcode_0.3.0 extrafont_0.19
[100] gdtools_0.3.7 tibble_3.2.1 BiocManager_1.30.23
[103] multcompView_0.1-10 cli_3.6.3 xtable_1.8-4
[106] parameters_0.22.1 systemfonts_1.1.0 munsell_0.5.1
[109] Rcpp_1.0.13 zeallot_0.1.0 png_0.1-8
[112] parallel_4.4.1 assertthat_0.2.1 bayestestR_0.14.0
[115] Rmpfr_0.9-5 mvtnorm_1.3-1 scales_1.3.0
[118] insight_0.20.3 purrr_1.0.2 crayon_1.5.3
[121] GetoptLong_1.0.5 rlang_1.1.4 TSP_1.2-4